Reproduce graphs from original data

igraph / igraphdata

Data sets for the igraph R package

http://igraph.org/r

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Reproduce graphs from original data #8

Open krlmlr opened 1 year ago

krlmlr commented 1 year ago

Done by inst/getdata.R, I have trouble recreating yeast and USairports .

The Nature publications required for yeast are not found, cannot open URL 'https://www.nature.com/nature/journal/v417/n6887/extref/nature750-s1.doc': HTTP status was '404 Not Found', new location linked at https://www.nature.com/articles/nature750#Sec8
USairports relies on ~/Downloads/1067890998_T_T100D_SEGMENT_ALL_CARRIER.csv

@gaborcsardi: Can you help with the .csv file?

Moving forward, I propose to separate the downloads from the creation of the graphs so that we're less reliant on external data storage here.

gaborcsardi commented 1 year ago

I don't have that CSV any more, sorry.

krlmlr commented 1 year ago

Thanks. We could create that CSV from the graph, I suppose.

I'm thrilled that the other graphs seem to be recreatable without problems. We'll need to compare the results, though.

szhorvat commented 1 year ago

Just to understand, is it necessary to recreate the networks from the original source or are you just testing the scripts that do so?

krlmlr commented 1 year ago

No, it's not necessary, just good practice.

maelle commented 1 year ago

@krlmlr

Moving forward, I propose to separate the downloads from the creation of the graphs so that we're less reliant on external data storage here.

Do you mean the package should contain a copy of the datasets? Or we store them somewhere else?

krlmlr commented 1 year ago

I don't mind a copy of the raw data on GitHub.

maelle commented 1 year ago

so the task is to try and locate the yeast and airport data?

how do we compare the obtained graphs?

maelle commented 1 year ago

reg the yeast data, it probably is in https://www.nature.com/articles/nature750 but I don't have access (and even if we get access I suppose the data isn't really free to share :sweat_smile: )

maelle commented 1 year ago

oh wait this is the data: https://static-content.springer.com/esm/art%3A10.1038%2Fnature750/MediaObjects/41586_2002_BFnature750_MOESM2_ESM.doc (via https://www.nature.com/articles/nature750#Sec8)

krlmlr commented 1 year ago

Yes, yeast seems solved. The only tricky challenge is to reverse-engineer the CSV file, but I'm not sure it's worth it.

maelle commented 1 year ago

so what are the TODOs?

krlmlr commented 1 year ago

Find a place for the raw files in this repo
Split the getdata.R script, perhaps one unified download script, and one script per dataset?
Make sure that the generated data is unchanged

maelle commented 1 year ago

Wait so we need 3 new issues, this issue is not really closed then?

krlmlr commented 1 year ago

One issue is fine.